Global Transcriptome Sequencing Using the Illumina Platform and the Development of EST-SSR Markers in Autotetraploid Alfalfa
- Publication Date
- December 12, 2013
- Journal
- PLOS ONE
- Authors
- Zhipeng Liu, Tianlong Chen, Lichao Ma, Zhiguang Zhao, et al
- Volume
- 8
- Issue
- 12
- Pages
- e83549
- DOI
- https://dx.plos.org/10.1371/journal.pone.0083549
- Publisher URL
- http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0083549
- PubMed
- http://www.ncbi.nlm.nih.gov/pubmed/24349529
- PubMed Central
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3861513
- Europe PMC
- http://europepmc.org/abstract/MED/24349529
- Web of Science
- 000328731800126
- Scopus
- 84892576614
- Mendeley
- http://www.mendeley.com/research/global-transcriptome-sequencing-using-illumina-platform-development-estssr-markers-autotetraploid-al
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Mendeley | Further Information
{"title"=>"Global transcriptome sequencing using the illumina platform and the development of EST-SSR markers in autotetraploid alfalfa", "type"=>"journal", "authors"=>[{"first_name"=>"Zhipeng", "last_name"=>"Liu", "scopus_author_id"=>"55606268700"}, {"first_name"=>"Tianlong", "last_name"=>"Chen", "scopus_author_id"=>"56006317100"}, {"first_name"=>"Ma", "last_name"=>"Lichao", "scopus_author_id"=>"57199676053"}, {"first_name"=>"Zhiguang", "last_name"=>"Zhao", "scopus_author_id"=>"22837396800"}, {"first_name"=>"Patrick X.", "last_name"=>"Zhao", "scopus_author_id"=>"35265529600"}, {"first_name"=>"Zhibiao", "last_name"=>"Nan", "scopus_author_id"=>"55606321600"}, {"first_name"=>"Yanrong", "last_name"=>"Wang", "scopus_author_id"=>"7601514335"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84892576614", "doi"=>"10.1371/journal.pone.0083549", "pui"=>"372134047", "issn"=>"19326203", "pmid"=>"24349529", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84892576614"}, "id"=>"07e555a1-9ec7-331d-9ff2-48e9e958dbda", "abstract"=>"BACKGROUND: Alfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. The large size and complexity of the alfalfa genome has delayed the development of genomic resources for alfalfa research. Second-generation Illumina transcriptome sequencing is an efficient method for generating a global transcriptome sequence dataset for gene discovery and molecular marker development in alfalfa.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: More than 28 million sequencing reads (5.64 Gb of clean nucleotides) were generated by Illumina paired-end sequencing from 15 different alfalfa tissue samples. In total, 40,433 unigenes with an average length of 803 bp were obtained by de novo assembly. Based on a sequence similarity search of known proteins, a total of 36,684 (90.73%) unigenes were annotated. In addition, 1,649 potential EST-SSRs were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 100 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 82 were able to amplify sequences in initial screening tests, and 27 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 10 alfalfa accessions.\\n\\nCONCLUSIONS/SIGNIFICANCE: The present study provided global sequence data for autotetraploid alfalfa and demonstrates the Illumina platform is a fast and effective approach to EST-SSR markers development in alfalfa. The use of these transcriptome datasets will serve as a valuable public information platform to accelerate studies of the alfalfa genome.", "link"=>"http://www.mendeley.com/research/global-transcriptome-sequencing-using-illumina-platform-development-estssr-markers-autotetraploid-al", "reader_count"=>22, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Master"=>8, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Master"=>8, "Other"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>2, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Belgium"=>1, "Brazil"=>1, "Portugal"=>1}, "group_count"=>0}CrossRef
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Scopus | Further Information
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Relative Metric
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